Command-line options

Command line interface for stdvoidsim - Lovecraftian population genetic simulations.

usage: stdvoidsim [-h] [-V] [-v | -q] [-c CACHE_DIR] [-e {msprime,slim}]
                  [--msprime-model {hudson,dtwf,smc,smc_prime}]
                  [--msprime-change-model T MODEL] [--slim-path PATH]
                  [--slim-script] [--slim-scaling-factor Q] [--slim-burn-in X]
                  {AzaPri,BybWor,CatUlt,ChaFau,ColOos,CthGre,DagGod,DagHyd,DarYou,DhoGno,DimSha,EldThi,FirVam,FlyPol,ForSpa,GhaShe,GhoFee,GnpKeh,GugsUn,HasKin,HouFir,HunTin,LenSpi,MiGFun,MooFun,NigMan,NyaAza,RatThi,SanDre,SanDwl,SerHum,ShbNig,ShoNig,StarSp,TsaCho,TsaGod,WamUnd,YitGre,YogSot,ZooGul,download-genetic-maps}
                  ...

Positional Arguments

subcommand

Possible choices: AzaPri, BybWor, CatUlt, ChaFau, ColOos, CthGre, DagGod, DagHyd, DarYou, DhoGno, DimSha, EldThi, FirVam, FlyPol, ForSpa, GhaShe, GhoFee, GnpKeh, GugsUn, HasKin, HouFir, HunTin, LenSpi, MiGFun, MooFun, NigMan, NyaAza, RatThi, SanDre, SanDwl, SerHum, ShbNig, ShoNig, StarSp, TsaCho, TsaGod, WamUnd, YitGre, YogSot, ZooGul, download-genetic-maps

Named Arguments

-V, --version

show program’s version number and exit

-v, --verbose

Increase logging verbosity (can use be used multiple times).

Default: 1

-q, --quiet

Do not write any non-essential messages

-c, --cache-dir

Set the cache directory to the specified value. Note that this can also be set using the environment variable STDPOPSIM_CACHE. If both the environment variable and this option are set, the option takes precedence. Default: /home/docs/.cache/stdvoidsim

-e, --engine

Possible choices: msprime, slim

Specify a simulation engine.

Default: 'msprime'

msprime specific parameters

--msprime-model

Possible choices: hudson, dtwf, smc, smc_prime

Specify the simulation model used by msprime. See msprime API documentation for details.

Default: 'hudson'

--msprime-change-model

Change to the specified simulation MODEL at generation T. This option may provided multiple times.

Default: []

SLiM specific parameters

--slim-path

Full path to `slim’ executable.

--slim-script

Write script to stdout and exit without running SLiM.

Default: False

--slim-scaling-factor

Rescale model parameters by Q to speed up simulation. See SLiM manual: 5.5 Rescaling population sizes to improve simulation performance. [default=1].

Default: 1

--slim-burn-in

Length of the burn-in phase, in units of N generations [default=10].

Default: 10

Sub-commands

AzaPri

Run simulations for Azathoth primordia using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Azathoth primordia: Generation time: 1000000 Population size: 1 Mutation rate: 3.5e-11 Recombination rate: 1e-12

stdvoidsim AzaPri [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, nuclear_chaos_element

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, nuclear_chaos_element. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: NuclearPulsation_1S22, VoidEmanation_2S22

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: NuclearPulsation_1S22, VoidEmanation_2S22. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

BybWor

Run simulations for Byakhee voidwing using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Byakhee voidwing: Generation time: 10 Population size: 200000 Mutation rate: 4e-09 Recombination rate: 3e-09

stdvoidsim BybWor [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, II, chr2, III, chr3, IV, chr4, V, chr5, VI, chr6, void_organelle, chrM

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, VI, void_organelle. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: VoidSwarm_1M33, StarSystemSplit_2M33

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: VoidSwarm_1M33, StarSystemSplit_2M33. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

CatUlt

Run simulations for Felis ultharensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Felis ultharensis: Generation time: 5 Population size: 100000 Mutation rate: 2e-08 Recombination rate: 1.5e-08

stdvoidsim CatUlt [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, chr1, whisker_1, 2, chr2, whisker_2, 3, chr3, claw_pair, 4, chr4, tail_segment, 5, chr5, night_vision, 6, chr6, dream_sense, dream_mitogenome, mt, dream_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, dream_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: UltharProtection_1C20, DreamlandsPatrol_2C20

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: UltharProtection_1C20, DreamlandsPatrol_2C20. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

ChaFau

Run simulations for Chaugnarus faugnis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Chaugnarus faugnis: Generation time: 10000 Population size: 200 Mutation rate: 2e-10 Recombination rate: 1e-10

stdvoidsim ChaFau [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, proboscis_major, II, chr2, tusk_pair, III, chr3, vampire_organ, IV, chr4, stone_hide, V, chr5, temporal_gland, proboscis_plasmid, mt, feeding_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, proboscis_plasmid. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: HillShrine_1L32, MigrationFromAsia_2L32

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: HillShrine_1L32, MigrationFromAsia_2L32. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

ColOos

Run simulations for Chromatis extraspatiala using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Chromatis extraspatiala: Generation time: 0.1 Population size: 10000 Mutation rate: 1.002e-06 Recombination rate: 4.999e-07

stdvoidsim ColOos [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, II, spectral_element

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, spectral_element. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: MeteorBloom_1G27, WellSpread_2G27

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: MeteorBloom_1G27, WellSpread_2G27. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

CthGre

Run simulations for Cthulhu greatoldone using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Cthulhu greatoldone: Generation time: 10000 Population size: 500 Mutation rate: 1e-10 Recombination rate: 1e-09

stdvoidsim CthGre [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, tentacle_1, II, chr2, tentacle_2, III, chr3, wing_pair, IV, chr4, cephalopod_segment, V, chr5, void_linker, VI, chr6, elder_sign, psychic_plasmid, mt, dream_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, VI, psychic_plasmid. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: DeepSlumber_1R28, RlyehRising_2P20

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: DeepSlumber_1R28, RlyehRising_2P20. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

DagGod

Run simulations for Dagonus maximus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Dagonus maximus: Generation time: 50000 Population size: 50 Mutation rate: 5e-11 Recombination rate: 3e-11

stdvoidsim DagGod [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, titan_arm_1, II, chr2, titan_arm_2, III, chr3, deep_gill_pair, IV, chr4, scale_matrix, V, chr5, bioluminescence, VI, chr6, pressure_organ, VII, chr7, trench_sensor, VIII, chr8, spawn_gland, IX, chr9, abyssal_cortex, X, chr10, elder_memory, abyssal_plasmid, mt, abyssal_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, VI, VII, VIII, IX, X, abyssal_plasmid. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: AbyssalSlumber_1O31, DeepOneProgenitor_2O31

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: AbyssalSlumber_1O31, DeepOneProgenitor_2O31. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

DagHyd

Run simulations for Dagonus hydridae using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Dagonus hydridae: Generation time: 100 Population size: 50000 Mutation rate: 3e-08 Recombination rate: 1.5e-08

stdvoidsim DagHyd [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, abyssal_mitogenome, MT

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, abyssal_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: InnsmouthDecline_1M27, HybridIntrogression_2M27

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: InnsmouthDecline_1M27, HybridIntrogression_2M27. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

DarYou

Run simulations for Obscurus silvanus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Obscurus silvanus: Generation time: 50 Population size: 35000 Mutation rate: 2e-08 Recombination rate: 1.5e-08

stdvoidsim DarYou [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, trunk_1, II, chr2, trunk_2, III, chr3, trunk_3, IV, chr4, trunk_4, V, chr5, trunk_5, VI, chr6, trunk_6, root_organelle, mt, dark_root

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, VI, root_organelle. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: ForestExpansion_1B35, MotherSpawn_2B35

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: ForestExpansion_1B35, MotherSpawn_2B35. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

DhoGno

Run simulations for Dholos subterraneus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Dholos subterraneus: Generation time: 200 Population size: 15000 Mutation rate: 4.001e-09 Recombination rate: 7e-09

stdvoidsim DhoGno [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, II, III, IV, V, VI, segment_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, VI, segment_organelle. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: DeepTunnels_1C26, SurfaceBreak_2C26

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: DeepTunnels_1C26, SurfaceBreak_2C26. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

DimSha

Run simulations for Dimensius shambleris using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Dimensius shambleris: Generation time: 100 Population size: 3000 Mutation rate: 8.002e-09 Recombination rate: 1e-08

stdvoidsim DimSha [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, II, III, planar_element

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, planar_element. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: PlanarDrift_1B33, PlaneSplit_2B33

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: PlanarDrift_1B33, PlaneSplit_2B33. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

EldThi

Run simulations for Elderium antarcticae using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Elderium antarcticae: Generation time: 1000 Population size: 10000 Mutation rate: 1e-09 Recombination rate: 5e-10

stdvoidsim EldThi [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, II, chr2, III, chr3, IV, chr4, V, chr5, stellar_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, stellar_organelle. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: CivilizationCollapse_1D31, AntarcticRetreat_2L30

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: CivilizationCollapse_1D31, AntarcticRetreat_2L30. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

FirVam

Run simulations for Igneus vampirus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Igneus vampirus: Generation time: 0.01 Population size: 1000000 Mutation rate: 5e-06 Recombination rate: 9.999e-07

stdvoidsim FirVam [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, flame_segment_1, II, chr2, flame_segment_2, plasma_element, mt, plasma_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, plasma_element. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: StarfireBurst_1D36, CthughaSpawn_2D36

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: StarfireBurst_1D36, CthughaSpawn_2D36. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

FlyPol

Run simulations for Polypus volantis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Polypus volantis: Generation time: 2000 Population size: 20000 Mutation rate: 6.002e-09 Recombination rate: 7.999e-09

stdvoidsim FlyPol [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, II, III, IV, wind_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, wind_organelle. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: YithianWar_1P35, SurfaceRaid_2P35

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: YithianWar_1P35, SurfaceRaid_2P35. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

ForSpa

Run simulations for Informis generatus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Informis generatus: Generation time: 10 Population size: 25000 Mutation rate: 3e-08 Recombination rate: 2e-08

stdvoidsim ForSpa [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, protoplasm_segment_1, II, chr2, protoplasm_segment_2, III, chr3, protoplasm_segment_3, amorphous_element, mt, amorphous_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, amorphous_element. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: CavernSpawning_1S31, TempleGuardians_2S31

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: CavernSpawning_1S31, TempleGuardians_2S31. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

GhaShe

Run simulations for Ghastus cavernicola using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Ghastus cavernicola: Generation time: 3 Population size: 80000 Mutation rate: 1.8e-08 Recombination rate: 2e-08

stdvoidsim GhaShe [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, carrion_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, carrion_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: ValeOfPnath_1C26, UpperCaves_2C26

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: ValeOfPnath_1C26, UpperCaves_2C26. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

GhoFee

Run simulations for Ghoulish necrophagus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Ghoulish necrophagus: Generation time: 20 Population size: 30000 Mutation rate: 1.5e-08 Recombination rate: 1.2e-08

stdvoidsim GhoFee [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, crypt_mitogenome, MT

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, crypt_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: SubterraneanIsolation_1P26, DreamlandsPassage_2P26

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: SubterraneanIsolation_1P26, DreamlandsPassage_2P26. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

GnpKeh

Run simulations for Gnophkehus arcticus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Gnophkehus arcticus: Generation time: 40 Population size: 12000 Mutation rate: 4e-09 Recombination rate: 3e-09

stdvoidsim GnpKeh [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, horn_segment, II, chr2, limb_pair_1, III, chr3, limb_pair_2, IV, chr4, limb_pair_3, V, chr5, fur_segment, VI, chr6, frost_segment, frost_mitogenome, mt, frost_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, VI, frost_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: HyperboreanIceAge_1H33, ArcticSplit_2H33

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: HyperboreanIceAge_1H33, ArcticSplit_2H33. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

GugsUn

Run simulations for Gugus underworldis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Gugus underworldis: Generation time: 30 Population size: 25000 Mutation rate: 5.001e-09 Recombination rate: 6e-09

stdvoidsim GugsUn [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, II, III, IV, gug_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, gug_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: VaultExile_1C26, TowerSplit_2C26

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: VaultExile_1C26, TowerSplit_2C26. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

HasKin

Run simulations for Hastur carcosensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Hastur carcosensis: Generation time: 50 Population size: 2000 Mutation rate: 5e-08 Recombination rate: 3e-08

stdvoidsim HasKin [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, II, chr2, III, chr3, IV, chr4, V, chr5, VI, chr6, VII, chr7, yellow_sign_element, YSE

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, VI, VII, yellow_sign_element. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: YellowSignSpread_1C95, CarcosaEarth_2C95

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: YellowSignSpread_1C95, CarcosaEarth_2C95. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

HouFir

Run simulations for Houndus tindalosi using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Houndus tindalosi: Generation time: 500 Population size: 5000 Mutation rate: 3.001e-09 Recombination rate: 4.999e-09

stdvoidsim HouFir [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, II, III, angular_genome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, angular_genome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: AngularTime_1L29, CornerEmergence_2L29

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: AngularTime_1L29, CornerEmergence_2L29. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

HunTin

Run simulations for Venator obscurus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Venator obscurus: Generation time: 20 Population size: 15000 Mutation rate: 6e-09 Recombination rate: 4e-09

stdvoidsim HunTin [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, serpentine_1, II, chr2, serpentine_2, III, chr3, serpentine_3, IV, chr4, serpentine_4, shadow_element, mt, dark_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, shadow_element. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: DarkFlight_1M33, NyarlathService_2M33

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: DarkFlight_1M33, NyarlathService_2M33. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

LenSpi

Run simulations for Araneus lengensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Araneus lengensis: Generation time: 10 Population size: 20000 Mutation rate: 1e-08 Recombination rate: 7.999e-09

stdvoidsim LenSpi [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, silk_1, II, chr2, silk_2, III, chr3, silk_3, IV, chr4, silk_4, V, chr5, silk_5, silk_mitogenome, mt, silk_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, silk_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: PlateauDominion_1C26, WebNetwork_2C26

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: PlateauDominion_1C26, WebNetwork_2C26. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

MiGFun

Run simulations for Migo fungoides using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Migo fungoides: Generation time: 5 Population size: 500000 Mutation rate: 2e-08 Recombination rate: 1e-08

stdvoidsim MiGFun [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, II, chr2, III, chr3, IV, chr4, V, chr5, spore_plasmid, plasmid1

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, spore_plasmid. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: YuggothColony_1A30, InterplanetarySpread_2A30

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: YuggothColony_1A30, InterplanetarySpread_2A30. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

MooFun

Run simulations for Lunaris bestialis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Lunaris bestialis: Generation time: 8 Population size: 45000 Mutation rate: 1.2e-08 Recombination rate: 1.5e-08

stdvoidsim MooFun [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, II, III, IV, lunar_element

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, lunar_element. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: DarkSideDominion_1C26, TradeFleet_2C26

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: DarkSideDominion_1C26, TradeFleet_2C26. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

NigMan

Run simulations for Nightgauntus mantaformis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Nightgauntus mantaformis: Generation time: 5 Population size: 75000 Mutation rate: 2e-08 Recombination rate: 1.8e-08

stdvoidsim NigMan [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, II, III, IV, V, VI, faceless_element

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, VI, faceless_element. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: NgranekFlock_1C26, DreamVoidSplit_2C26

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: NgranekFlock_1C26, DreamVoidSplit_2C26. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

NyaAza

Run simulations for Nyarlathotep azathothspawn using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Nyarlathotep azathothspawn: Generation time: 1 Population size: 1000 Mutation rate: 1e-07 Recombination rate: 1e-06

stdvoidsim NyaAza [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, II, III, IV, V, VI, VII, VIII, chaos_fragment

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, VI, VII, VIII, chaos_fragment. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: ThousandMasks_1W19, ChaosSpread_2D21

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: ThousandMasks_1W19, ChaosSpread_2D21. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

RatThi

Run simulations for Rattus magicus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Rattus magicus: Generation time: 1 Population size: 50000 Mutation rate: 2e-08 Recombination rate: 1.5e-08

stdvoidsim RatThi [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, chr1, familiar_segment_1, 2, chr2, familiar_segment_2, 3, chr3, familiar_segment_3, 4, chr4, humanface_segment, 5, chr5, paw_segment, 6, chr6, tail_segment, 7, chr7, whisker_segment, witch_mitogenome, mt, witch_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, witch_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: WitchHousePlague_1G32, FamiliarLineage_2G32

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: WitchHousePlague_1G32, FamiliarLineage_2G32. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

SanDre

Run simulations for Shantakus dreamlandis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Shantakus dreamlandis: Generation time: 15 Population size: 60000 Mutation rate: 1.5e-08 Recombination rate: 2e-08

stdvoidsim SanDre [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, II, III, IV, V, scale_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, scale_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: KadathNesting_1C26, LengSplit_2C26

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: KadathNesting_1C26, LengSplit_2C26. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

SanDwl

Run simulations for Arenicola abyssalis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Arenicola abyssalis: Generation time: 15 Population size: 40000 Mutation rate: 1.2e-08 Recombination rate: 9e-09

stdvoidsim SanDwl [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, burrow_segment_1, II, chr2, burrow_segment_2, III, chr3, desiccation_arm, IV, chr4, sand_filter, desert_element, mt, desert_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, desert_element. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: DesertBurrowers_1A730, IremRuins_2A730

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: DesertBurrowers_1A730, IremRuins_2A730. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

SerHum

Run simulations for Serpentis valusiensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Serpentis valusiensis: Generation time: 50 Population size: 40000 Mutation rate: 1e-08 Recombination rate: 1.2e-08

stdvoidsim SerHum [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, 6, 7, venom_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, venom_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: ValusianEmpire_1K29, Infiltration_2K29

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: ValusianEmpire_1K29, Infiltration_2K29. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

ShbNig

Run simulations for Shubniggurath fertilitas using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Shubniggurath fertilitas: Generation time: 25 Population size: 100000 Mutation rate: 3e-08 Recombination rate: 2.5e-08

stdvoidsim ShbNig [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, II, III, IV, V, VI, VII, VIII, IX, fertility_plasmid

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, VI, VII, VIII, IX, fertility_plasmid. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: ThousandYoung_1W27, CultBreeding_2W27

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: ThousandYoung_1W27, CultBreeding_2W27. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

ShoNig

Run simulations for Shoggoth nigrumplasma using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Shoggoth nigrumplasma: Generation time: 0.5 Population size: 100000 Mutation rate: 5e-09 Recombination rate: 2e-08

stdvoidsim ShoNig [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, II, chr2, III, chr3, IV, chr4, V, chr5, VI, chr6, VII, chr7, VIII, chr8, IX, chr9, X, chr10, XI, chr11, XII, chr12

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, VI, VII, VIII, IX, X, XI, XII. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: AntarcticRevolt_1D31, CityRuins_2D31

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: AntarcticRevolt_1D31, CityRuins_2D31. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

StarSp

Run simulations for Starspawn cthulhidae using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Starspawn cthulhidae: Generation time: 5000 Population size: 10000 Mutation rate: 2e-09 Recombination rate: 5e-09

stdvoidsim StarSp [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, II, III, IV, V, spawn_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, spawn_organelle. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: SunkenCity_1J26, XothMigration_2J26

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: SunkenCity_1J26, XothMigration_2J26. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

TsaCho

Run simulations for Tsathoggua choriensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Tsathoggua choriensis: Generation time: 25 Population size: 70000 Mutation rate: 1.5e-08 Recombination rate: 1.2e-08

stdvoidsim TsaCho [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, chr1, tainted_1, 2, chr2, tainted_2, 3, chr3, tainted_3, 4, chr4, tainted_4, 5, chr5, tainted_5, 6, chr6, tainted_6, 7, chr7, tainted_7, 8, chr8, tainted_8, tainted_mitogenome, mt, dark_mt

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, tainted_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: PlateauTribes_1D33, TaintedLineage_2D33

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: PlateauTribes_1D33, TaintedLineage_2D33. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

TsaGod

Run simulations for Tsathoggua somnolentis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Tsathoggua somnolentis: Generation time: 50000 Population size: 100 Mutation rate: 5e-10 Recombination rate: 3e-10

stdvoidsim TsaGod [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, toad_segment_1, II, chr2, toad_segment_2, III, chr3, sloth_segment, IV, chr4, cavern_segment, nkai_plasmid, mt, nkai_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, nkai_plasmid. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: SlothfulDormancy_1S31, NkaiCaverns_2S31

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: SlothfulDormancy_1S31, NkaiCaverns_2S31. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

WamUnd

Run simulations for Degeneratus subterraneus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Degeneratus subterraneus: Generation time: 10 Population size: 20000 Mutation rate: 3e-08 Recombination rate: 2e-08

stdvoidsim WamUnd [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, chr1, tunnel_segment_1, 2, chr2, tunnel_segment_2, 3, chr3, claw_arm, 4, chr4, jaw_segment, 5, chr5, night_eye, 6, chr6, burrow_sense, 7, chr7, degenerate_limb, 8, chr8, vestigial_cortex, degenerate_mitogenome, mt, degenerate_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, degenerate_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: MartenseDegeneration_1M22, CatskillWarrens_2M22

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: MartenseDegeneration_1M22, CatskillWarrens_2M22. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

YitGre

Run simulations for Yithianus temporalis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Yithianus temporalis: Generation time: 500 Population size: 50000 Mutation rate: 3e-09 Recombination rate: 2e-09

stdvoidsim YitGre [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, chr1, cone_1, II, chr2, cone_2, III, chr3, cone_3, IV, chr4, cone_4, V, chr5, cone_5, VI, chr6, cone_6, VII, chr7, cone_7, temporal_organelle, mt, time_organelle

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, VI, VII, temporal_organelle. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: TemporalMigration_1P35, ConicMindSwap_2P35

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: TemporalMigration_1P35, ConicMindSwap_2P35. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

YogSot

Run simulations for Yogsothoth dimensionalis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Yogsothoth dimensionalis: Generation time: 100000 Population size: 10 Mutation rate: 1e-12 Recombination rate: 1e-11

stdvoidsim YogSot [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: I, II, III, dimensional_loop

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, dimensional_loop. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: DimensionalEchoes_1W28, DunwichLineage_2W28

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: DimensionalEchoes_1W28, DunwichLineage_2W28. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

ZooGul

Run simulations for Zoogus sylvaticus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.

Default population parameters for Zoogus sylvaticus: Generation time: 2 Population size: 500000 Mutation rate: 2.501e-08 Recombination rate: 3e-08

stdvoidsim ZooGul [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
                  [-c] [-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
                  [-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
                  [-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
                  [--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
                  samples [samples ...]

Positional Arguments

samples

The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.

Named Arguments

--help-models

Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models

-b, --bibtex-file

Write citations to a given bib file. This will overwrite the file.

-D, --dry-run

Do not run actual simulation

Default: False

-c, --chromosome

Possible choices: 1, 2, 3, 4, 5, forest_mitogenome

Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, forest_mitogenome. Default=None.

-L, --length

Simulate a default contig of given length.

-i, --inclusion-mask

Path to inclusion mask specified in bed format.

-e, --exclusion-mask

Path to exclusion mask specified in bed format.

-l, --length-multiplier

Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.

--left

The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).

--right

The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.

-s, --seed

The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.

--keep-mutation-ids-as-alleles

If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.

Default: False

-d, --demographic-model

Possible choices: EnchantedWood_1C26, DreamlandsSpread_2C26

Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: EnchantedWood_1C26, DreamlandsSpread_2C26. Please see –help-models for details of these models.

--dfe

Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.

--dfe-interval

Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.

--dfe-bed-file

A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.

-o, --output

Where to write the output tree sequence file. Defaults to stdout if not specified

download-genetic-maps

Download genetic maps and store them in the cache directory. Maps are downloaded regardless of whether they are already in the cache or not. Please use the –cache-dir option to download maps to a specific directory.

stdvoidsim download-genetic-maps [-h] [species] [genetic_maps ...]

Positional Arguments

species

Download genetic maps for this species. If not specified download all known genetic maps.

genetic_maps

If specified, download these genetic maps. If no maps are provided, download all maps for this species.